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24 BIOLOGICAL REPORT 29 Periodicity Chart Jon Feb Mar Apt May Jun JuI Aug Sept Oct Nov Dee Adults - summer - winter - spawning Fry Juvenile I H Fig. 4.1. Species periodicity chart. In developing the Index of Biological Integrity (lBI), Gorman and Karr (1978) suggested that hu- man-induced impacts to river systems fall into five major categories. Table 4.2 (as modified from Karr 1991) identifies food source, water quality, habitat structure, flow regime, and biotic interactions as equally important, but very different, mechanisms by which human activities can alter the biotic in- tegrity of running-water ecosystems. The IFIM modeling approach has been influenced by this view of river system impacts, and models have been developed that fit within Karr's paradigm, as dis- cussed below. Flow Regime During the 1950's and 1960's, construction of large storage reservoirs and massive withdrawal systems for irrigation in the western United States focused IFIM developers on techniques for evaluat- ~g changes ~ flo~ regime. Today, the most sophis- ticated modelmg m the area of flow regime com- bines ideas from hydraulic engineering, river flood routing, and habitat-use behavior of fish with em- pirically measured calibration flows. Hydraulic simulation models allow for accurate prediction of water surface elevations, water depth, and water velocity at points in the water column and at vari- ous points across a river channel. Models allow simulations of these variables for many unmeas- ured discharges (Millious et al. 1989). Such simu- lations allow the analyst to evaluate the duration and timing of inundation of th~ aquatic-terrestrial transition zone (ATI'Z; Junk etal. 1989). The flow regime is also recognized as critical for channel maintenance, both in terms of maintaining habitat structure (e.g., stream width, riparian vegetation) and in flushing fine sediment out of graveVcobble channels. (U.S. Forest Service 1984) , Habitat Structure The influence of human-induced activity on habitat structure (channel-floodplain geometry) has been one of the most neglected areas of stream ecology (Hill et al. 1991). At present, riverine geo- morphology is at the forefront of descriptive ecol- ogy, and much work is in progress. A prime exam- ple is the effort of the U.S. Army Corps of Engineers to restore floodplain channel connec- tions along river corridors that have been severely impacted through river entrainment for naviga- tion and reservoir operations. The classification of mesohabitat types, and the association of impor- tant species and life history events to those specific habitats, underscores the importance of ade- quately describing and manipulating channel mor- phology as a component of river management. Many riverine species throughout the United States are rapidly declining, and many species are proposed for listing as threatened or endangered. The loss of side channel, backwater, and edge habitats has been a primary reason for this decline (Hesse and Sheets 1993). There are no predictive habitat structure or channel models acceptable for evaluating flow regime in terms of the active chan- nel response. Crude calculations of the extent of aggradation or degradation (Fig. 4.2) at selected cross sections below a large reservoir are possible but cannot be used to forecast channel widening, edge habitat building, or floodplain cutting. There has been much empirical research on the protec- tion of existing channels (Stalnaker et al. 1989) and restoration of floodplain habitats (Hesse and Sheets 1993). Recently, researchers have focused interest on flushing flows as part of river manage- ment regime for flushing silts and sands from within the interstitial spaces among gravel and cobbles in trout and salmon streams (Reiser et al. 1989). This research is now progressing into the laboratory and, along with field studies, should provide algorithms suitable for computing the amount and timing offlow pulses for flushing fines from river reaches below large reservoirs. Water Quality There are sophisticated and well-developed water quality models (Bartholow 1989; Thornton et al. 1990). Water chemistry, dissolved oxygen (DO), and temperature can be very accurately pre- dicted throughout a stream network system as a function of reservoir operations and water routing. However, modeling emphasis has been largely to